<html lang="en">

  <head>
    <META content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
    <meta charset="UTF-8"/>
    <meta content="width=device-width, initial-scale=1" name="viewport"/>
    <title>Jvarkit : Java utilities for Bioinformatics</title>
    <link href="/jvarkit/assets/css/style.css" rel="stylesheet"/>
  </head>

<body>
<div class="container markdown-body">
<h1>Jvarkit : Java utilities for Bioinformatics</h1>
<a href="https://travis-ci.org/lindenb/jvarkit"><img src="https://travis-ci.org/lindenb/jvarkit.svg"/></a><br/>

<h2>Tools</h2>
<table>

<thead>
	
<tr>
		
		<th>Name</th>
		<th>Description</th>
		<th>Keywords</th>
		<th>Terms</th>
		<th>Misc</th>
	
</tr>

</thead>

<tbody>

<tr id="samjs"><th><a href="SamJavascript.html" title="SamJavascript">samjs</a></th><td>Filters a BAM using a javascript expression ( java nashorn engine  ).</td><td>sam bam nashorn javascript filter</td><td/><td/></tr>
<tr id="casectrljfx"><th><a href="CaseControlJfx.html" title="CaseControlJfx">casectrljfx</a></th><td>chart of case/control maf from a VCF and a pedigree</td><td>vcf pedigree case control visualization jfx chart maf</td><td/><td/></tr>
<tr id="pubmedcodinglang"><th><a href="PubmedCodingLanguages.html" title="PubmedCodingLanguages">pubmedcodinglang</a></th><td>Programming language use distribution from recent programs / articles</td><td>pubmed xml code programming</td><td/><td/></tr>
<tr id="vcffixindels"><th><a href="VCFFixIndels.html" title="VCFFixIndels">vcffixindels</a></th><td>Fix samtools indels (for @SolenaLS)</td><td>vcf indel</td><td/><td><span style="color:orange;" title="deprecated">use `bcftools norm`</span>. </td></tr>
<tr id="vcftail"><th><a href="VcfTail.html" title="VcfTail">vcftail</a></th><td>print the last variants of a vcf</td><td>vcf</td><td/><td/></tr>
<tr id="vcfhead"><th><a href="VcfHead.html" title="VcfHead">vcfhead</a></th><td>print the first variants of a vcf</td><td>vcf</td><td/><td/></tr>
<tr id="vcfmulti2oneallele"><th><a href="VcfMultiToOneAllele.html" title="VcfMultiToOneAllele">vcfmulti2oneallele</a></th><td>'one variant with N ALT alleles' to 'N variants with one ALT'</td><td>vcf</td><td/><td/></tr>
<tr id="vcfin"><th><a href="VcfIn.html" title="VcfIn">vcfin</a></th><td>Only prints variants that are contained/not contained into another VCF</td><td>vcf compare</td><td/><td/></tr>
<tr id="vcfpredictions"><th><a href="VCFPredictions.html" title="VCFPredictions">vcfpredictions</a></th><td>Basic Variant Effect prediction using gtf</td><td>vcf annotation prediction gtf</td><td/><td/></tr>
<tr id="vcffilterso"><th><a href="VcfFilterSequenceOntology.html" title="VcfFilterSequenceOntology">vcffilterso</a></th><td>Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user's SO-terms will be also used.</td><td>vcf filter sequenceontology prediction so</td><td/><td/></tr>
<tr id="vcffilterjs"><th><a href="VCFFilterJS.html" title="VCFFilterJS">vcffilterjs</a></th><td>Filtering VCF with javascript expressions</td><td>vcf filter javascript json nashorn</td><td/><td/></tr>
<tr id="vcfpolyx"><th><a href="VCFPolyX.html" title="VCFPolyX">vcfpolyx</a></th><td>Number of repeated REF bases around POS.</td><td>vcf repeat</td><td/><td/></tr>
<tr id="vcfbed"><th><a href="VCFBed.html" title="VCFBed">vcfbed</a></th><td>Transfer information from a BED to a VCF</td><td>bed vcf annotation</td><td/><td/></tr>
<tr id="vcftrio"><th><a href="VCFTrios.html" title="VCFTrios">vcftrio</a></th><td>Find mendelian incompatibilitie / denovo variants in a VCF</td><td>vcf mendelian pedigree denovo</td><td/><td/></tr>
<tr id="groupbygene"><th><a href="GroupByGene.html" title="GroupByGene">groupbygene</a></th><td>Group VCF data by gene/transcript. By default it uses data from VEP , SnpEff</td><td>vcf gene</td><td/><td/></tr>
<tr id="addlinearindextobed"><th><a href="AddLinearIndexToBed.html" title="AddLinearIndexToBed">addlinearindextobed</a></th><td>Use a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart.</td><td>bed reference</td><td/><td/></tr>
<tr id="almostsortedvcf"><th><a href="AlmostSortedVcf.html" title="AlmostSortedVcf">almostsortedvcf</a></th><td>Sort an 'almost' sorted VCF. Most variants should be sorted but a few  consecutive lines might have been switched by a caller.</td><td/><td/><td/></tr>
<tr id="backlocate"><th><a href="BackLocate.html" title="BackLocate">backlocate</a></th><td>Mapping a mutation on a protein back to the genome.</td><td>vcf annotation prediction protein</td><td/><td/></tr>
<tr id="bam2fastq"><th><a href="BamToFastq.html" title="BamToFastq">bam2fastq</a></th><td>Same as picard/SamToFastq but allow missing reads + shuffle reads using hash(name) so you can use them with bwa. </td><td>fastq</td><td/><td><span style="color:orange;" title="deprecated">use picard</span>. </td></tr>
<tr id="bam2raster"><th><a href="Bam2Raster.html" title="Bam2Raster">bam2raster</a></th><td>BAM to raster graphics</td><td>bam alignment graphics visualization png</td><td/><td/></tr>
<tr id="bam2svg"><th><a href="BamToSVG.html" title="BamToSVG">bam2svg</a></th><td>BAM to Scalar Vector Graphics (SVG)</td><td>bam alignment graphics visualization svg</td><td/><td/></tr>
<tr id="bam2xml"><th><a href="Bam2Xml.html" title="Bam2Xml">bam2xml</a></th><td>converts a BAM to XML</td><td>sam bam xml</td><td/><td/></tr>
<tr id="bam2wig"><th><a href="Bam2Wig.html" title="Bam2Wig">bam2wig</a></th><td>Bam to fixedStep Wiggle converter , or BED GRAPH. Parses the cigar String to get the depth. Memory intensive: must alloc sizeof(int)*size(chrom)</td><td>bam wig wiggle bed</td><td/><td/></tr>
<tr id="bamcmpcoverage"><th><a href="BamCmpCoverage.html" title="BamCmpCoverage">bamcmpcoverage</a></th><td>Creates the figure of a comparative view of the depths sample vs sample. Memory consideration: the tool alloc an array of bits which size is: (MIN(maxdepth-mindepth,pixel_width_for_one_sample) * count_samples)^2</td><td>sam bam visualization coverage</td><td/><td/></tr>
<tr id="bamrenamechr"><th><a href="ConvertBamChromosomes.html" title="ConvertBamChromosomes">bamrenamechr</a></th><td>Convert the names of the chromosomes in a BAM file</td><td>sam bam chromosome contig</td><td/><td/></tr>
<tr id="bamstats04"><th><a href="BamStats04.html" title="BamStats04">bamstats04</a></th><td>Coverage statistics for a BED file.</td><td>sam bam coverage depth statistics bed</td><td/><td/></tr>
<tr id="bamstats05"><th><a href="BamStats05.html" title="BamStats05">bamstats05</a></th><td>Coverage statistics for a BED file, group by gene</td><td>bam coverage statistics bed</td><td/><td/></tr>
<tr id="batchigvpictures"><th><a href="BatchIGVPictures.html" title="BatchIGVPictures">batchigvpictures</a></th><td/><td/><td/><td/></tr>
<tr id="bedliftover"><th><a href="BedLiftOver.html" title="BedLiftOver">bedliftover</a></th><td>Lift-over a VCF file</td><td>bed liftover</td><td/><td/></tr>
<tr id="bedrenamechr"><th><a href="ConvertBedChromosomes.html" title="ConvertBedChromosomes">bedrenamechr</a></th><td>Convert the names of the chromosomes in a Bed file</td><td>bed chromosome contig convert</td><td/><td/></tr>
<tr id="biostar103303"><th><a href="Biostar103303.html" title="Biostar103303">biostar103303</a></th><td>Calculate Percent Spliced In (PSI).</td><td>sam bam psi</td><td/><td/></tr>
<tr id="biostar130456"><th><a href="Biostar130456.html" title="Biostar130456">biostar130456</a></th><td>Split individual VCF files from multisamples VCF file</td><td>vcf samples sample</td><td/><td/></tr>
<tr id="biostar59647"><th><a href="Biostar59647.html" title="Biostar59647">biostar59647</a></th><td>SAM/BAM to XML</td><td>sam bam xml</td><td/><td/></tr>
<tr id="biostar76892"><th><a href="Biostar76892.html" title="Biostar76892">biostar76892</a></th><td>fix strand of two paired reads close but on the same strand. </td><td>sam bam</td><td/><td/></tr>
<tr id="biostar77288"><th><a href="Biostar77288.html" title="Biostar77288">biostar77288</a></th><td>Low resolution sequence alignment visualization</td><td>bam sam visualization svg alignment</td><td/><td/></tr>
<tr id="biostar77828"><th><a href="Biostar77828.html" title="Biostar77828">biostar77828</a></th><td>Divide the human genome among X cores, taking into account gaps</td><td>workflow reference parallel</td><td/><td/></tr>
<tr id="biostar78285"><th><a href="Biostar78285.html" title="Biostar78285">biostar78285</a></th><td>Extract BAMs coverage as a VCF file.</td><td>sam bam depth coverage</td><td/><td/></tr>
<tr id="biostar78400"><th><a href="Biostar78400.html" title="Biostar78400">biostar78400</a></th><td>add the read group info to the sam file on a per lane basis</td><td>sam bam xml read-group</td><td/><td/></tr>
<tr id="biostar81455"><th><a href="Biostar81455.html" title="Biostar81455">biostar81455</a></th><td>Defining precisely the exonic genomic context based on a position .</td><td>bed gene gtf</td><td/><td/></tr>
<tr id="biostar84452"><th><a href="Biostar84452.html" title="Biostar84452">biostar84452</a></th><td>remove clipped bases from a BAM file</td><td>sam bam clip</td><td/><td/></tr>
<tr id="biostar84786"><th><a href="Biostar84786.html" title="Biostar84786">biostar84786</a></th><td>Matrix transposition</td><td>matrix util</td><td/><td/></tr>
<tr id="biostar86363"><th><a href="Biostar86363.html" title="Biostar86363">biostar86363</a></th><td>Set genotype of specific sample/genotype comb to unknown in multisample vcf file. See http://www.biostars.org/p/86363/</td><td>sample genotype vcf</td><td/><td/></tr>
<tr id="biostar86480"><th><a href="Biostar86480.html" title="Biostar86480">biostar86480</a></th><td>Genomic restriction finder</td><td>rebase genome enzyme restricion genome</td><td/><td/></tr>
<tr id="biostar90204"><th><a href="Biostar90204.html" title="Biostar90204">biostar90204</a></th><td>Bam version of linux split.</td><td>sam bam split util</td><td/><td/></tr>
<tr id="msa2vcf"><th><a href="MsaToVcf.html" title="MsaToVcf">msa2vcf</a></th><td>Getting a VCF file from a CLUSTAW or a FASTA alignment. </td><td>vcf snp msa alignment</td><td/><td><span style="color:orange;" title="deprecated">use https://github.com/sanger-pathogens/snp_sites</span>. </td></tr>
<tr id="biostar95652"><th><a href="Biostar95652.html" title="Biostar95652">biostar95652</a></th><td>Drawing a schematic genomic context tree.</td><td>genbank svg tree evolution</td><td/><td/></tr>
<tr id="biostar139647"><th><a href="Biostar139647.html" title="Biostar139647">biostar139647</a></th><td>Convert alignment in Fasta/Clustal format to SAM/BAM file</td><td>msa sam bam clustal</td><td/><td/></tr>
<tr id="biostar145820"><th><a href="Biostar145820.html" title="Biostar145820">biostar145820</a></th><td>subsample/shuffle BAM to fixed number of alignments.</td><td>sam bam shuffle</td><td/><td/></tr>
<tr id="blastmapannots"><th><a href="BlastMapAnnotations.html" title="BlastMapAnnotations">blastmapannots</a></th><td>Maps uniprot/genbank annotations on a blast result.</td><td>blast annotation genbank uniprot</td><td/><td/></tr>
<tr id="buildwpontology"><th><a href="BuildWikipediaOntology.html" title="BuildWikipediaOntology">buildwpontology</a></th><td>Build a simple RDFS/XML ontology from the Wikipedia Categories</td><td>wikipedia ontology rdf gui</td><td/><td/></tr>
<tr id="bwamemdigest"><th><a href="BWAMemDigest.html" title="BWAMemDigest">bwamemdigest</a></th><td/><td/><td/><td/></tr>
<tr id="bwamemnop"><th><a href="BWAMemNOp.html" title="BWAMemNOp">bwamemnop</a></th><td>Merge the other BWA-MEM alignements with its SA:Z:* attributes to an alignment containing a cigar string with 'N' (  Skipped region from the reference.)</td><td>bwa sam bam</td><td/><td/></tr>
<tr id="cmpbams"><th><a href="CompareBams.html" title="CompareBams">cmpbams</a></th><td>Compare two or more BAM files</td><td>sam bam compare</td><td/><td/></tr>
<tr id="cmpbamsandbuild"><th><a href="CompareBamAndBuild.html" title="CompareBamAndBuild">cmpbamsandbuild</a></th><td>Compare two  BAM files mapped on two different builds. Requires a liftover chain file</td><td/><td/><td/></tr>
<tr id="coveragenormalizer"><th><a href="CoverageNormalizer.html" title="CoverageNormalizer">coveragenormalizer</a></th><td>normalize BAM coverage</td><td/><td/><td/></tr>
<tr id="downsamplevcf"><th><a href="DownSampleVcf.html" title="DownSampleVcf">downsamplevcf</a></th><td>DownSample a VCF. Will keep 'n' random variants in a vcf.</td><td>vcf</td><td/><td/></tr>
<tr id="evs2vcf"><th><a href="EvsToVcf.html" title="EvsToVcf">evs2vcf</a></th><td>Download data from EVS http://evs.gs.washington.edu/EVS as a BED chrom/start/end/XML For later use, see VCFTabixml.</td><td/><td/><td/></tr>
<tr id="evsdumpxml"><th><a href="EvsDumpXml.html" title="EvsDumpXml">evsdumpxml</a></th><td>Download data from EVS http://evs.gs.washington.edu/EVS as XML file.</td><td/><td/><td/></tr>
<tr id="fastq2fasta"><th><a href="FastqToFasta.html" title="FastqToFasta">fastq2fasta</a></th><td>fastq -&gt; fasta</td><td>fastq fasta</td><td/><td><span style="color:orange;" title="deprecated">use awk, samtools...</span>. </td></tr>
<tr id="kg2bed"><th><a href="KnownGenesToBed.html" title="KnownGenesToBed">kg2bed</a></th><td>converts UCSC knownGenes file to BED.</td><td>ucsc bed knownGenes</td><td/><td/></tr>
<tr id="fastqentropy"><th><a href="FastqEntropy.html" title="FastqEntropy">fastqentropy</a></th><td>Compute the Entropy of a Fastq file (distribution of the length(gzipped(sequence))</td><td>fastq</td><td/><td/></tr>
<tr id="fastqgrep"><th><a href="FastqGrep.html" title="FastqGrep">fastqgrep</a></th><td>Grep reads names in fastq</td><td>fastq</td><td/><td><span style="color:orange;" title="deprecated">use picard</span>. </td></tr>
<tr id="fastqjs"><th><a href="FastqJavascript.html" title="FastqJavascript">fastqjs</a></th><td>Filters a FASTQ file using javascript( java nashorn engine). </td><td>fastq</td><td/><td/></tr>
<tr id="fastqphred64to33"><th><a href="ConvertPhred64toFastq33.html" title="ConvertPhred64toFastq33">fastqphred64to33</a></th><td>Convert Illumina Fastq 64 encoding to Fastq 33</td><td>fastq</td><td/><td/></tr>
<tr id="fastqrevcomp"><th><a href="FastqRevComp.html" title="FastqRevComp">fastqrevcomp</a></th><td>produces a reverse-complement fastq (for mate pair alignment see http://seqanswers.com/forums/showthread.php?t=5085 )</td><td>fastq</td><td/><td/></tr>
<tr id="fastqshuffle"><th><a href="FastqShuffle.html" title="FastqShuffle">fastqshuffle</a></th><td>Shuffle Fastq files</td><td>fastq</td><td/><td/></tr>
<tr id="fastqsplitinterleaved"><th><a href="FastqSplitInterleaved.html" title="FastqSplitInterleaved">fastqsplitinterleaved</a></th><td>Split interleaved Fastq files.</td><td>fastq</td><td/><td/></tr>
<tr id="findallcoverageatposition"><th><a href="FindAllCoverageAtPosition.html" title="FindAllCoverageAtPosition">findallcoverageatposition</a></th><td>Find depth at specific position in a list of BAM files. My colleague Estelle asked: in all the BAM we sequenced, can you give me the depth at a given position ?</td><td>bam coverage search depth</td><td/><td/></tr>
<tr id="findavariation"><th><a href="FindAVariation.html" title="FindAVariation">findavariation</a></th><td>Finds a specific mutation in a list of VCF files</td><td>vcf variation search find bcf</td><td/><td/></tr>
<tr id="findcorruptedfiles"><th><a href="FindCorruptedFiles.html" title="FindCorruptedFiles">findcorruptedfiles</a></th><td>Reads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ/BED/TBI/BAI)</td><td>vcf bam fastq bed</td><td/><td/></tr>
<tr id="findmyvirus"><th><a href="FindMyVirus.html" title="FindMyVirus">findmyvirus</a></th><td>Find my Virus. Created for Adrien Inserm. Proportion of reads mapped on HOST/VIRUS.</td><td>bam virus</td><td/><td/></tr>
<tr id="findnewsplicesites"><th><a href="FindNewSpliceSites.html" title="FindNewSpliceSites">findnewsplicesites</a></th><td>use the 'N' operator in the cigar string to find unknown splice sites</td><td>bam sam rnaseq splice gtf</td><td/><td/></tr>
<tr id="fixvarscanmissingheader "><th><a href="FixVarScanMissingVCFHeader.html" title="FixVarScanMissingVCFHeader">fixvarscanmissingheader </a></th><td>Fix the sample name in the #CHROM header and fix VCF header missingh in varscan2. Sometimes, but not always, it happends. See  http://seqanswers.com/forums/showthread.php?t=33235 </td><td/><td/><td/></tr>
<tr id="fixvcf"><th><a href="FixVCF.html" title="FixVCF">fixvcf</a></th><td>Fix a VCF if INFO or FILTER are missing</td><td/><td/><td/></tr>
<tr id="fixvcfformat"><th><a href="FixVcfFormat.html" title="FixVcfFormat">fixvcfformat</a></th><td>Fix PL format in VCF. Problem is described in http://gatkforums.broadinstitute.org/discussion/3453</td><td/><td/><td/></tr>
<tr id="fixvcfmissinggenotypes"><th><a href="FixVcfMissingGenotypes.html" title="FixVcfMissingGenotypes">fixvcfmissinggenotypes</a></th><td>After a VCF-merge, read a VCF, look back at some BAMS to tells if the missing genotypes were homozygotes-ref or not-called. If the number of reads is greater than min.depth, then a missing genotype is said hom-ref.</td><td>sam bam vcf sv genotype</td><td/><td/></tr>
<tr id="gcpercentanddepth"><th><a href="GcPercentAndDepth.html" title="GcPercentAndDepth">gcpercentanddepth</a></th><td>Extracts GC% and depth for multiple bam using a sliding window</td><td>gc% depth coverage</td><td/><td/></tr>
<tr id="genomicjaspar"><th><a href="GenomicJaspar.html" title="GenomicJaspar">genomicjaspar</a></th><td>Find jaspar patterns in FASTA sequences. Reports a BED file.</td><td>jaspar genomic pattern</td><td/><td/></tr>
<tr id="howmanybamdict"><th><a href="HowManyBamDict.html" title="HowManyBamDict">howmanybamdict</a></th><td>finds if there's are some differences in the sequence dictionaries.</td><td>sam bam dict vcf</td><td/><td/></tr>
<tr id="illuminadir"><th><a href="IlluminaDirectory.html" title="IlluminaDirectory">illuminadir</a></th><td>Create a structured (**JSON** or **XML**) representation of a directory containing some Illumina FASTQs.</td><td>json xml illumina fastq workflow</td><td/><td/></tr>
<tr id="ilmnfastqstats"><th><a href="IlluminaStatsFastq.html" title="IlluminaStatsFastq">ilmnfastqstats</a></th><td>Reads filenames from stdin: Count FASTQs in Illumina Result.</td><td/><td/><td/></tr>
<tr id="impactofduplicates"><th><a href="ImpactOfDuplicates.html" title="ImpactOfDuplicates">impactofduplicates</a></th><td>Impact of Duplicates per BAM.</td><td>bam</td><td/><td/></tr>
<tr id="liftover2svg"><th><a href="LiftOverToSVG.html" title="LiftOverToSVG">liftover2svg</a></th><td>Convert LiftOver chain files to animated SVG</td><td>svg liftover ucsc xml</td><td/><td/></tr>
<tr id="mapuniprot"><th><a href="MapUniProtFeatures.html" title="MapUniProtFeatures">mapuniprot</a></th><td>map uniprot features on reference genome</td><td>uniprot bed fasta reference xjc xml</td><td/><td/></tr>
<tr id="mergesplittedblast"><th><a href="MergeSplittedBlast.html" title="MergeSplittedBlast">mergesplittedblast</a></th><td>merge blast Hits from splitted BLAST database</td><td>blast</td><td/><td/></tr>
<tr id="ncbitaxonomy2xml"><th><a href="NcbiTaxonomyToXml.html" title="NcbiTaxonomyToXml">ncbitaxonomy2xml</a></th><td>Dump NCBI taxonomy tree as a hierarchical XML document</td><td>taxonomy ncbi xml</td><td/><td/></tr>
<tr id="samjmx"><th><a href="SamJmx.html" title="SamJmx">samjmx</a></th><td>Monitor/interrupt/break a BAM/SAM stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html</td><td>sam bam jmx monitoring</td><td/><td/></tr>
<tr id="ngsfilessummary"><th><a href="NgsFilesSummary.html" title="NgsFilesSummary">ngsfilessummary</a></th><td>Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). Useful to get a summary of your samples.</td><td>sam bam vcf util</td><td/><td/></tr>
<tr id="noemptyvcf"><th><a href="NoEmptyVCF.html" title="NoEmptyVCF">noemptyvcf</a></th><td>If VCF is empty or doesn't exists, create a dummy one</td><td/><td/><td><span style="color:orange;" title="deprecated">Was developped at the time where VEP didn't send an output if there was no variant, just a header in the source vcf.</span>. </td></tr>
<tr id="nozerovariationvcf"><th><a href="NoZeroVariationVCF.html" title="NoZeroVariationVCF">nozerovariationvcf</a></th><td>cat a whole VCF, or, if there is no variant, creates a fake one</td><td>vcf</td><td/><td/></tr>
<tr id="pademptyfastq"><th><a href="PadEmptyFastq.html" title="PadEmptyFastq">pademptyfastq</a></th><td>Pad empty fastq sequence/qual with N/#</td><td>fastq</td><td/><td><span style="color:orange;" title="deprecated">use awk</span>. </td></tr>
<tr id="pubmeddump"><th><a href="PubmedDump.html" title="PubmedDump">pubmeddump</a></th><td>Dump XML results from pubmed/Eutils</td><td>ncbi pubmed xml</td><td/><td/></tr>
<tr id="pubmedorcidgraph"><th><a href="PubmedOrcidGraph.html" title="PubmedOrcidGraph">pubmedorcidgraph</a></th><td>Creates a graph from Pubmed and Authors' Orcid identifiers</td><td>pubmed ncbi orcid</td><td/><td/></tr>
<tr id="pubmedfilterjs"><th><a href="PubmedFilterJS.html" title="PubmedFilterJS">pubmedfilterjs</a></th><td>Filters Pubmed XML with a javascript  (java rhino) expression. Context contain 'article' a  PubmedBookArticle or a PubmedArticle and 'index', the index in the XML file.</td><td>pubmed javascript xml ncbi</td><td/><td/></tr>
<tr id="referencetovcf"><th><a href="ReferenceToVCF.html" title="ReferenceToVCF">referencetovcf</a></th><td>Creates a VCF containing all the possible substitutions from a Reference Genome.</td><td>vcf reference fasta</td><td/><td/></tr>
<tr id="sam2json"><th><a href="SamToJson.html" title="SamToJson">sam2json</a></th><td>Convert a SAM input to JSON</td><td>sam bam json</td><td/><td/></tr>
<tr id="sam2psl"><th><a href="SamToPsl.html" title="SamToPsl">sam2psl</a></th><td>Convert SAM/BAM to PSL http://genome.ucsc.edu/FAQ/FAQformat.html#format2 or BED12</td><td>sam bam psl</td><td/><td><span style="color:orange;" title="deprecated">use bedtools/bamtobed</span>. </td></tr>
<tr id="sam2tsv"><th><a href="Sam2Tsv.html" title="Sam2Tsv">sam2tsv</a></th><td>Prints the SAM alignments as a TAB delimited file.</td><td>sam bam table cram tsv</td><td/><td/></tr>
<tr id="sam4weblogo"><th><a href="SAM4WebLogo.html" title="SAM4WebLogo">sam4weblogo</a></th><td>Sequence logo for different alleles or generated from SAM/BAM </td><td>sam bam visualization logo</td><td/><td/></tr>
<tr id="Samclipindelfraction"><th><a href="SamClipIndelFraction.html" title="SamClipIndelFraction">Samclipindelfraction</a></th><td>Extract clipping/indel fraction from BAM</td><td>sam bam clip</td><td/><td><span style="color:orange;" title="deprecated">This tool can be replace with Bioalcidaejdk</span>. </td></tr>
<tr id="samextractclip"><th><a href="SamExtractClip.html" title="SamExtractClip">samextractclip</a></th><td>Extract Soft Clipped Sequences from a SAM. Ouput is a FASTQ</td><td>sam bam fastq clip</td><td/><td/></tr>
<tr id="samfixcigar"><th><a href="SamFixCigar.html" title="SamFixCigar">samfixcigar</a></th><td>Fix Cigar String in SAM replacing 'M' by 'X' or '='</td><td>sam bam cigar</td><td/><td/></tr>
<tr id="samgrep"><th><a href="SamGrep.html" title="SamGrep">samgrep</a></th><td>grep read-names in a bam file</td><td>sam bam</td><td/><td/></tr>
<tr id="samshortinvert"><th><a href="SamShortInvertion.html" title="SamShortInvertion">samshortinvert</a></th><td>Scan short inversions in SAM using supplementary reads.</td><td>sam bam sv inversion</td><td/><td/></tr>
<tr id="samstats01"><th><a href="BamStats01.html" title="BamStats01">samstats01</a></th><td>Statistics about the reads in a BAM.</td><td>sam bam</td><td/><td/></tr>
<tr id="sortvcfoninfo"><th><a href="SortVcfOnInfo.html" title="SortVcfOnInfo">sortvcfoninfo</a></th><td>Sort a VCF a field in the INFO column</td><td>vcf sort annotation</td><td/><td/></tr>
<tr id="sortvcfonref2"><th><a href="SortVcfOnRef2.html" title="SortVcfOnRef2">sortvcfonref2</a></th><td>Sort a VCF using the internal dictionary or an external reference order (Deprecated: use bcftools sort).</td><td>vcf sort</td><td/><td><span style="color:orange;" title="deprecated">use picard sortvcf</span>. </td></tr>
<tr id="splitbytile"><th><a href="SplitByTile.html" title="SplitByTile">splitbytile</a></th><td>Split Bam By tile</td><td>sam bam</td><td/><td/></tr>
<tr id="vcf2hilbert"><th><a href="VcfToHilbert.html" title="VcfToHilbert">vcf2hilbert</a></th><td>Plot a Hilbert Curve from a VCF file.</td><td>vcf image visualization</td><td/><td/></tr>
<tr id="vcf2postscript"><th><a href="VcfToPostscript.html" title="VcfToPostscript">vcf2postscript</a></th><td>Print VCF context as Postscript</td><td>vcf postscript</td><td/><td/></tr>
<tr id="vcf2rdf"><th><a href="VcfToRdf.html" title="VcfToRdf">vcf2rdf</a></th><td>convert VCF to RDF (N3 notation)</td><td>vcf rdf</td><td/><td/></tr>
<tr id="vcf2sql"><th><a href="VcfToSql.html" title="VcfToSql">vcf2sql</a></th><td>Generate the SQL code to insert a VCF into mysql</td><td>vcf sql</td><td/><td/></tr>
<tr id="vcf2xml"><th><a href="Vcf2Xml.html" title="Vcf2Xml">vcf2xml</a></th><td>Convert VCF to XML</td><td>vcf xml</td><td/><td/></tr>
<tr id="vcfbiomart"><th><a href="VcfBiomart.html" title="VcfBiomart">vcfbiomart</a></th><td>BiomartQueries with VCF</td><td>vcf ensembl biomart annotation</td><td/><td/></tr>
<tr id="vcfcadd"><th><a href="VcfCadd.html" title="VcfCadd">vcfcadd</a></th><td>Annotate VCF with  Combined Annotation Dependent Depletion (CADD) (Kircher &amp; al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.PubMed PMID: 24487276.</td><td>vcf prediction cadd annotation</td><td/><td/></tr>
<tr id="vcfcmppred"><th><a href="VCFComparePredictions.html" title="VCFComparePredictions">vcfcmppred</a></th><td>Compare predictions (SNPEff, VEP) for several VCFs</td><td/><td/><td/></tr>
<tr id="vcfcomm"><th><a href="VCFComm.html" title="VCFComm">vcfcomm</a></th><td>Equivalent of linux comm for VCF</td><td/><td/><td/></tr>
<tr id="vcfcompare"><th><a href="VCFCompare.html" title="VCFCompare">vcfcompare</a></th><td>Compares two VCF files</td><td>vcf compare</td><td/><td/></tr>
<tr id="vcfcomparegt"><th><a href="VCFCompareGT.html" title="VCFCompareGT">vcfcomparegt</a></th><td> compare two or more genotype-callers for the same individuals. Produce a VCF with FORMAT fields indicating if a genotype is new or modified.</td><td>vcf compare</td><td/><td/></tr>
<tr id="vcfconcat"><th><a href="VcfConcat.html" title="VcfConcat">vcfconcat</a></th><td>Concatenante sorted VCF with same sample, does NOT merge genotypes</td><td>vcf</td><td/><td/></tr>
<tr id="vcfcutsamples"><th><a href="VcfCutSamples.html" title="VcfCutSamples">vcfcutsamples</a></th><td>Select/Exclude some samples from a VCF</td><td>vcf sample</td><td/><td><span style="color:orange;" title="deprecated">use bcftools or gatk SelectVariants</span>. </td></tr>
<tr id="vcfjaspar"><th><a href="VcfJaspar.html" title="VcfJaspar">vcfjaspar</a></th><td>Finds JASPAR profiles in VCF</td><td>vcf matrix jaspar</td><td/><td/></tr>
<tr id="vcfliftover"><th><a href="VcfLiftOver.html" title="VcfLiftOver">vcfliftover</a></th><td>Lift-over a VCF file</td><td>vcf liftover</td><td/><td/></tr>
<tr id="vcfmerge"><th><a href="VCFMerge.html" title="VCFMerge">vcfmerge</a></th><td>Merge a large number of VCF Files</td><td>vcf sort merge</td><td/><td/></tr>
<tr id="vcfmulti2one"><th><a href="VcfMultiToOne.html" title="VcfMultiToOne">vcfmulti2one</a></th><td>Convert VCF with multiple samples to a VCF with one SAMPLE, duplicating variant and adding the sample name in the INFO column</td><td>vcf sample</td><td/><td/></tr>
<tr id="vcfregulomedb"><th><a href="VcfRegulomeDB.html" title="VcfRegulomeDB">vcfregulomedb</a></th><td>Annotate a VCF with the Regulome data (http://regulome.stanford.edu/</td><td/><td/><td/></tr>
<tr id="vcfrenamechr"><th><a href="ConvertVcfChromosomes.html" title="ConvertVcfChromosomes">vcfrenamechr</a></th><td>Convert the names of the chromosomes in a VCF file</td><td>vcf contig chromosome convert</td><td/><td><span style="color:orange;" title="deprecated">use `bcftools annotate` with `--rename-chrs file`</span>. </td></tr>
<tr id="vcfrenamesamples"><th><a href="VcfRenameSamples.html" title="VcfRenameSamples">vcfrenamesamples</a></th><td>Rename the Samples in a VCF</td><td>vcf sample</td><td/><td/></tr>
<tr id="vcfresetvcf"><th><a href="VcfRemoveGenotypeIfInVcf.html" title="VcfRemoveGenotypeIfInVcf">vcfresetvcf</a></th><td>Reset Genotypes in VCF (./.) if they've been found in another VCF indexed with tabix</td><td>vcf genotype</td><td/><td/></tr>
<tr id="vcfsetdict"><th><a href="VcfSetSequenceDictionary.html" title="VcfSetSequenceDictionary">vcfsetdict</a></th><td>Set the `##contig` lines in a VCF header on the fly</td><td>vcf dict fai</td><td/><td/></tr>
<tr id="vcfshuffle"><th><a href="VCFShuffle.html" title="VCFShuffle">vcfshuffle</a></th><td>Shuffle a VCF</td><td>vcf</td><td/><td/></tr>
<tr id="vcfSimulator"><th><a href="VcfSimulator.html" title="VcfSimulator">vcfSimulator</a></th><td>Generate a VCF</td><td>vcf</td><td/><td/></tr>
<tr id="vcfstats"><th><a href="VcfStats.html" title="VcfStats">vcfstats</a></th><td>Produce VCF statitics</td><td>vcf stats burden gnuplot</td><td/><td/></tr>
<tr id="vcfcombinetwosnvs"><th><a href="VCFCombineTwoSnvs.html" title="VCFCombineTwoSnvs">vcfcombinetwosnvs</a></th><td>Detect Mutations than are the consequences of two distinct variants. This kind of variant might be ignored/skipped from classical variant consequence predictor. Idea from @SolenaLS and then @AntoineRimbert</td><td>vcf annotation prediction protein mnv</td><td/><td/></tr>
<tr id="vcfstripannot"><th><a href="VCFStripAnnotations.html" title="VCFStripAnnotations">vcfstripannot</a></th><td>Removes one or more field from the INFO/FORMAT column of a VCF.</td><td>vcf</td><td/><td><span style="color:orange;" title="deprecated">Use bcftools annotate -x </span>. </td></tr>
<tr id="vcftabixml"><th><a href="VCFTabixml.html" title="VCFTabixml">vcftabixml</a></th><td> annotate a value from a vcf+xml file</td><td>vcf xml</td><td/><td/></tr>
<tr id="vcfvcf"><th><a href="VcfVcf.html" title="VcfVcf">vcfvcf</a></th><td>Get the INFO from a VCF and use it for another VCF</td><td/><td/><td><span style="color:orange;" title="deprecated">obsolete. use GATK</span>. </td></tr>
<tr id="worldmapgenome"><th><a href="WorldMapGenome.html" title="WorldMapGenome">worldmapgenome</a></th><td>Genome/Map of the world. Input is a BED file: chrom/start/end/country.</td><td>gis</td><td/><td/></tr>
<tr id="uniprotfilterjs"><th><a href="UniprotFilterJS.html" title="UniprotFilterJS">uniprotfilterjs</a></th><td>Filters Uniprot DUMP+ XML with a javascript  (java rhino) expression. Context contain 'entry' an uniprot entry and 'index', the index in the XML file.</td><td>unitprot javascript xjc xml</td><td/><td/></tr>
<tr id="skipxmlelements"><th><a href="SkipXmlElements.html" title="SkipXmlElements">skipxmlelements</a></th><td>Filter XML elements with a javascript  (java rhino) expression. Context contain 'element' the current element. It implementsthe interface Tag described in  SkipXmlElements.class</td><td>xml javascript</td><td/><td/></tr>
<tr id="vcfensemblvep"><th><a href="VcfEnsemblVepRest.html" title="VcfEnsemblVepRest">vcfensemblvep</a></th><td>Annotate a VCF with ensembl REST API</td><td>vcf annotation rest ensembl xml xslt xsl</td><td/><td/></tr>
<tr id="vcfgroupbypop"><th><a href="VcfGroupByPopulation.html" title="VcfGroupByPopulation">vcfgroupbypop</a></th><td>Group VCF data by population, creates a VCF  where each 'SAMPLE' is a population</td><td>vcf pedigree population</td><td/><td/></tr>
<tr id="bamtile"><th><a href="BamTile.html" title="BamTile">bamtile</a></th><td>Answer to @sjackman : Is there a bedtools command to determine a minimal tiling path? A minimal set of features that cover a maximum of the target.</td><td>bam sam</td><td/><td/></tr>
<tr id="xcontaminations"><th><a href="XContaminations.html" title="XContaminations">xcontaminations</a></th><td>For @AdrienLeger2 : cross contamination between samples by looking at the homozygous genotypes.</td><td>sam bam vcf contamination</td><td/><td/></tr>
<tr id="biostar3654"><th><a href="Biostar3654.html" title="Biostar3654">biostar3654</a></th><td>show blast alignment with annotations</td><td>blast xml annotation</td><td/><td/></tr>
<tr id="vcfburden"><th><a href="VcfBurden.html" title="VcfBurden">vcfburden</a></th><td>Solena: vcf to (chrom/pos/ref/alt/individus(G:0/1/2/-9)</td><td/><td/><td><span style="color:orange;" title="deprecated">deprecated</span>. </td></tr>
<tr id="vcfreplacetag"><th><a href="VCFReplaceTag.html" title="VCFReplaceTag">vcfreplacetag</a></th><td>Replace the key for INFO/FORMAT/FILTER</td><td>vcf</td><td/><td><span style="color:orange;" title="deprecated">use `bcftools annotate` with option `-c`</span>. </td></tr>
<tr id="vcfpeekvcf"><th><a href="VcfPeekVcf.html" title="VcfPeekVcf">vcfpeekvcf</a></th><td>Get the INFO from a VCF and use it for another VCF</td><td>vcf annotation</td><td/><td/></tr>
<tr id="vcfgetvariantbyIndex"><th><a href="VcfGetVariantByIndex.html" title="VcfGetVariantByIndex">vcfgetvariantbyIndex</a></th><td>Access a Plain or BGZF-compressed VCF file by index</td><td>vcf</td><td/><td/></tr>
<tr id="vcfmulti2oneinfo"><th><a href="VcfMultiToOneInfo.html" title="VcfMultiToOneInfo">vcfmulti2oneinfo</a></th><td>'one INFO with N values' to 'N variants with one INFO'</td><td>vcf</td><td/><td/></tr>
<tr id="bedindextabix"><th><a href="BedIndexTabix.html" title="BedIndexTabix">bedindextabix</a></th><td>Index and sort a Bed on the fly with Tabix.</td><td>bed tabix</td><td/><td/></tr>
<tr id="vcf2bam"><th><a href="VcfToBam.html" title="VcfToBam">vcf2bam</a></th><td>vcf to bam</td><td>ref vcf bam</td><td/><td/></tr>
<tr id="vcffilterxpath"><th><a href="VcfFilterXPath.html" title="VcfFilterXPath">vcffilterxpath</a></th><td>Filter a VCF with a XPATH expression on a INFO tag containing a base64 encodede xml document</td><td>vcf xml xpath</td><td/><td/></tr>
<tr id="biostar140111"><th><a href="Biostar140111.html" title="Biostar140111">biostar140111</a></th><td>How to obtain human genotype data from dpSNP ftp?</td><td/><td/><td/></tr>
<tr id="extendrefwithreads"><th><a href="ExtendReferenceWithReads.html" title="ExtendReferenceWithReads">extendrefwithreads</a></th><td>Extending ends of sequences with the help of reads</td><td>read fastq reference sam bam</td><td/><td/></tr>
<tr id="pcrslicereads"><th><a href="PcrSliceReads.html" title="PcrSliceReads">pcrslicereads</a></th><td>Mark PCR reads to their PCR amplicon</td><td>pcr sam bam cigar</td><td/><td/></tr>
<tr id="vcfjmx"><th><a href="VcfJmx.html" title="VcfJmx">vcfjmx</a></th><td>Monitor/interrupt/break a VCF stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html</td><td>java jmx vcf</td><td/><td/></tr>
<tr id="gtf2xml"><th><a href="Gtf2Xml.html" title="Gtf2Xml">gtf2xml</a></th><td>Convert GTF/GFF to XML</td><td>xml gtf gff gff3</td><td/><td/></tr>
<tr id="sortsamrefname"><th><a href="SortSamRefName.html" title="SortSamRefName">sortsamrefname</a></th><td>Sort a BAM on chromosome/contig and then on read/querty name</td><td>sam sort</td><td/><td/></tr>
<tr id="biostar154220"><th><a href="Biostar154220.html" title="Biostar154220">biostar154220</a></th><td>Cap BAM to a given coverage</td><td>bam sam coverage depth</td><td/><td/></tr>
<tr id="biostar160470"><th><a href="Biostar160470.html" title="Biostar160470">biostar160470</a></th><td>Getting untranslated nucleotide sequences on tblastn standalone </td><td>blasn blast translation protein</td><td/><td/></tr>
<tr id="biostar165777"><th><a href="Biostar165777.html" title="Biostar165777">biostar165777</a></th><td>Split a XML file</td><td>xml</td><td/><td/></tr>
<tr id="vcfcomparecallers"><th><a href="VcfCompareCallers.html" title="VcfCompareCallers">vcfcomparecallers</a></th><td>Compare two VCFs and print common/exclusive information for each sample/genotype</td><td>vcf compare genotype</td><td/><td/></tr>
<tr id="bamclip2insertion"><th><a href="BamClipToInsertion.html" title="BamClipToInsertion">bamclip2insertion</a></th><td>Convert SOFT clip to Insertion of other read confirm it</td><td>sam bam clip</td><td/><td/></tr>
<tr id="biostar170742"><th><a href="Biostar170742.html" title="Biostar170742">biostar170742</a></th><td>convert sam format to axt Format</td><td>sam axt</td><td/><td/></tr>
<tr id="biostar172515"><th><a href="Biostar172515.html" title="Biostar172515">biostar172515</a></th><td>Convert BAI to XML</td><td>bai bam xml</td><td/><td/></tr>
<tr id="biostar173114"><th><a href="Biostar173114.html" title="Biostar173114">biostar173114</a></th><td>make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114/</td><td>sam bam</td><td/><td/></tr>
<tr id="biostar175929"><th><a href="Biostar175929.html" title="Biostar175929">biostar175929</a></th><td>Construct a combination set of fasta sequences from a vcf</td><td>fasta vcf</td><td/><td/></tr>
<tr id="vcfcalledwithanothermethod"><th><a href="VcfCalledWithAnotherMethod.html" title="VcfCalledWithAnotherMethod">vcfcalledwithanothermethod</a></th><td>Compare one vcf with other , add a flag to tell if a variant was called with another method. Vcf must be sorted on the same Dict.</td><td>vcf compare concordance</td><td/><td/></tr>
<tr id="biostar178713"><th><a href="Biostar178713.html" title="Biostar178713">biostar178713</a></th><td>split bed file into several bed files where each region is separated of any other by N bases</td><td>bed</td><td/><td/></tr>
<tr id="vcfremovegenotypejs"><th><a href="VcfRemoveGenotypeJs.html" title="VcfRemoveGenotypeJs">vcfremovegenotypejs</a></th><td>Reset Genotype in VCF using a javascript expression</td><td/><td/><td/></tr>
<tr id="bamstats02"><th><a href="BamStats02.html" title="BamStats02">bamstats02</a></th><td>Statistics about the flags and reads in a BAM</td><td>sam bam</td><td/><td/></tr>
<tr id="bamstats02view"><th><a href="BamStats02View.html" title="BamStats02View">bamstats02view</a></th><td>Statistics about the flags and reads in a BAM. Visualize date from BamStats02</td><td/><td/><td/></tr>
<tr id="biostar105754"><th><a href="Biostar105754.html" title="Biostar105754">biostar105754</a></th><td>bigwig : peak distance from specific genomic region</td><td>wig bigwig</td><td/><td/></tr>
<tr id="bam2sql"><th><a href="BamToSql.html" title="BamToSql">bam2sql</a></th><td>Convert a SAM/BAM to sqlite statements</td><td>bam sam sql sqlite</td><td/><td/></tr>
<tr id="vcf2zip"><th><a href="VcfToZip.html" title="VcfToZip">vcf2zip</a></th><td>Reads a stream of concatenated VCFs and insert them into a Zip file</td><td/><td/><td/></tr>
<tr id="pubmedgender"><th><a href="PubmedGender.html" title="PubmedGender">pubmedgender</a></th><td>Add gender-related attributes in the Author tag of pubmed xml. </td><td>pubmed gender ncbi xml</td><td/><td/></tr>
<tr id="pubmedmap"><th><a href="PubmedMap.html" title="PubmedMap">pubmedmap</a></th><td>Use Pubmed Author's Affiliation to map the authors in the world.</td><td>pubmed xml gis map</td><td/><td/></tr>
<tr id="splitvcf"><th><a href="SplitVcf.html" title="SplitVcf">splitvcf</a></th><td>split a vcf using a named list of intervals...</td><td>vcf</td><td/><td/></tr>
<tr id="forkvcf"><th><a href="ForkVcf.html" title="ForkVcf">forkvcf</a></th><td>Fork a VCF.</td><td/><td/><td/></tr>
<tr id="bim2vcf"><th><a href="BimToVcf.html" title="BimToVcf">bim2vcf</a></th><td>convert a .bim to a .vcf . For @FlorianeS44</td><td>bim vcf</td><td/><td/></tr>
<tr id="concatsam"><th><a href="ConcatSam.html" title="ConcatSam">concatsam</a></th><td>concat sam files</td><td>sam bam</td><td/><td/></tr>
<tr id="samreadlengthdistribution"><th><a href="SamReadLengthDistribution.html" title="SamReadLengthDistribution">samreadlengthdistribution</a></th><td>Sam read/insert length distribution</td><td>sam bam histogram</td><td/><td/></tr>
<tr id="biostar214299"><th><a href="Biostar214299.html" title="Biostar214299">biostar214299</a></th><td>Extract allele specific reads from bamfiles</td><td>sam bam variant snp</td><td/><td/></tr>
<tr id="cmpbams4"><th><a href="CompareBams4.html" title="CompareBams4">cmpbams4</a></th><td>Compare two BAM files. Print a tab-delimited report</td><td>sam bam compare</td><td/><td/></tr>
<tr id="biostar234081"><th><a href="Biostar234081.html" title="Biostar234081">biostar234081</a></th><td>convert extended CIGAR to regular CIGAR ('X','=' -&gt; 'M')</td><td>sam bam cigar</td><td/><td/></tr>
<tr id="vcfgnomad"><th><a href="VcfGnomad.html" title="VcfGnomad">vcfgnomad</a></th><td>Peek annotations from gnomad</td><td>vcf annotation gnomad</td><td/><td/></tr>
<tr id="vcf2svg"><th><a href="VcfToSvg.html" title="VcfToSvg">vcf2svg</a></th><td>write a vcf to svg , with gene context</td><td>vcf svg xlm visualization</td><td/><td/></tr>
<tr id="mergeblastxml"><th><a href="MergeBlastXml.html" title="MergeBlastXml">mergeblastxml</a></th><td>merge XML blast results (same Iteration/Iteration_query-def in multiple xml files</td><td>blast xml</td><td/><td/></tr>
<tr id="vcfannotwithbeacon"><th><a href="VcfAnnotWithBeacon.html" title="VcfAnnotWithBeacon">vcfannotwithbeacon</a></th><td>Annotate a VCF with ga4gh beacon</td><td>ga4gh beacon vcf annotation</td><td/><td/></tr>
<tr id="commbams"><th><a href="CommBams.html" title="CommBams">commbams</a></th><td>Equivalent of unix 'comm' for bams sorted on queryname</td><td>sam bam comm compare</td><td/><td/></tr>
<tr id="samscansplitreads"><th><a href="SamScanSplitReads.html" title="SamScanSplitReads">samscansplitreads</a></th><td>scan split reads</td><td>sam sv splitreads clip</td><td/><td/></tr>
<tr id="samretrieveseqandqual"><th><a href="SamRetrieveSeqAndQual.html" title="SamRetrieveSeqAndQual">samretrieveseqandqual</a></th><td>I have a query-sorted BAM file without read/qual sequences and a FASTQ file with the read/qual sequences. Is there a tool to add seq to BAM?  for @sjackman https://twitter.com/sjackman/status/575368165531611136</td><td/><td/><td/></tr>
<tr id="biostar234230"><th><a href="Biostar234230.html" title="Biostar234230">biostar234230</a></th><td>Sliding Window : discriminate partial and fully contained fragments (from a bam file)</td><td/><td/><td/></tr>
<tr id="biostar251649"><th><a href="Biostar251649.html" title="Biostar251649">biostar251649</a></th><td> Annotating the flanking bases of SNPs in a VCF file</td><td>vcf annotation sequence reference</td><td/><td/></tr>
<tr id="vcfbedsetfilter"><th><a href="VCFBedSetFilter.html" title="VCFBedSetFilter">vcfbedsetfilter</a></th><td>Set FILTER for VCF if intersects with BED.</td><td>vcf bed filter</td><td/><td/></tr>
<tr id="bamliftover"><th><a href="BamLiftOver.html" title="BamLiftOver">bamliftover</a></th><td>Lift-over a BAM file.</td><td>bam liftover</td><td/><td/></tr>
<tr id="blast2sam"><th><a href="BlastToSam.html" title="BlastToSam">blast2sam</a></th><td>Convert a **BLASTN-XML** input to SAM</td><td>sam blast</td><td/><td/></tr>
<tr id="reduceblast"><th><a href="ReduceBlast.html" title="ReduceBlast">reduceblast</a></th><td>Reduce the size of XML blast, by removing iterations that have no Hit</td><td>blast xml</td><td/><td/></tr>
<tr id="blastn2snp"><th><a href="BlastNToSnp.html" title="BlastNToSnp">blastn2snp</a></th><td>print indel/mismatch in a blastn stream</td><td>blast snp</td><td/><td/></tr>
<tr id="splitbam3"><th><a href="SplitBam3.html" title="SplitBam3">splitbam3</a></th><td>Split a BAM by chromosome group</td><td>sam bam split</td><td/><td/></tr>
<tr id="vcfindextabix"><th><a href="VcfIndexTabix.html" title="VcfIndexTabix">vcfindextabix</a></th><td>Index and sort a VCF on the fly with Tabix</td><td>vcf tabix</td><td/><td/></tr>
<tr id="blastfilterjs"><th><a href="BlastFilterJS.html" title="BlastFilterJS">blastfilterjs</a></th><td>Filters a BlastOutput with a javascript expression. The script injects each &lt;Hit&gt; as the variable 'blasthit'. The user script should return 'true' to keep the hit.</td><td>blast js javascript filter</td><td/><td/></tr>
<tr id="SamSlop"><th><a href="SamSlop.html" title="SamSlop">SamSlop</a></th><td>extends sam by 'x' bases using the reference sequence</td><td>sam bam</td><td/><td/></tr>
<tr id="vcfgenesplitter"><th><a href="VcfGeneSplitter.html" title="VcfGeneSplitter">vcfgenesplitter</a></th><td>Split VCF+VEP by gene/transcript.</td><td>genes vcf</td><td/><td/></tr>
<tr id="sammaskalignedbases"><th><a href="SamMaskAlignedBases.html" title="SamMaskAlignedBases">sammaskalignedbases</a></th><td>Mask bases aligned on Reference.</td><td/><td/><td/></tr>
<tr id="queue2make"><th><a href="QueueToMake.html" title="QueueToMake">queue2make</a></th><td>Convert Broad/Queue genomestrip Log stream to Makefile.</td><td/><td/><td/></tr>
<tr id="pcrclipreads"><th><a href="PcrClipReads.html" title="PcrClipReads">pcrclipreads</a></th><td>Soft clip bam files based on PCR target regions</td><td>sam bam pcr bed</td><td/><td/></tr>
<tr id="vcfeigen"><th><a href="VcfEigen01.html" title="VcfEigen01">vcfeigen</a></th><td>Annotator for the data of https://xioniti01.u.hpc.mssm.edu/v1.1/ : Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as made available by the ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance.</td><td>vcf annotation variant</td><td/><td/></tr>
<tr id="vcfmovefilterstoinfo"><th><a href="VcfMoveFiltersToInfo.html" title="VcfMoveFiltersToInfo">vcfmovefilterstoinfo</a></th><td>Move any FILTER to the INFO column. reset FILTER to PASS</td><td>vcf format info</td><td/><td/></tr>
<tr id="vcfburdenmaf"><th><a href="VcfBurdenMAF.html" title="VcfBurdenMAF">vcfburdenmaf</a></th><td>MAF for Cases / Controls </td><td>vcf burden maf case control</td><td/><td/></tr>
<tr id="vcfburdenfisherh"><th><a href="VcfBurdenFisherH.html" title="VcfBurdenFisherH">vcfburdenfisherh</a></th><td>Fisher Case /Controls per Variant</td><td>vcf burden fisher</td><td/><td/></tr>
<tr id="vcfinjectpedigree"><th><a href="VcfInjectPedigree.html" title="VcfInjectPedigree">vcfinjectpedigree</a></th><td>Injects a pedigree (.ped) file in the VCF header</td><td>vcf pedigree burden</td><td/><td/></tr>
<tr id="samcolortag"><th><a href="SamColorTag.html" title="SamColorTag">samcolortag</a></th><td>Add the UCSC 'YC' color tag in a BAM. See http://software.broadinstitute.org/software/igv/book/export/html/6 and http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html</td><td>sam bam metadata javascript igv visualization</td><td/><td/></tr>
<tr id="vcffilternotinpedigree"><th><a href="VcfFilterNotInPedigree.html" title="VcfFilterNotInPedigree">vcffilternotinpedigree</a></th><td>Adds a FILTER 'NotInPedigree' if the only not(homref) genotypes are not in a pedigree</td><td>burden vcf pedigree</td><td/><td/></tr>
<tr id="vcfburdenexac"><th><a href="VcfBurdenFilterExac.html" title="VcfBurdenFilterExac">vcfburdenexac</a></th><td>Burden filter 3 - Exac</td><td>vcf burden exac</td><td/><td/></tr>
<tr id="vcf2table"><th><a href="VcfToTable.html" title="VcfToTable">vcf2table</a></th><td>convert a vcf to a table, to ease display in the terminal</td><td>vcf table visualization</td><td/><td/></tr>
<tr id="vcfburdenfiltergenes"><th><a href="VcfBurdenFilterGenes.html" title="VcfBurdenFilterGenes">vcfburdenfiltergenes</a></th><td>Filter VEP/SnpEff Output from a list of genes.</td><td>gene vcf vep snpeff</td><td/><td/></tr>
<tr id="allelefreqcalc"><th><a href="AlleleFrequencyCalculator.html" title="AlleleFrequencyCalculator">allelefreqcalc</a></th><td>Allele Frequency Calculator</td><td>vcf af</td><td/><td><span style="color:orange;" title="deprecated">Use bioalcidae</span>. </td></tr>
<tr id="bamindexreadnames"><th><a href="BamIndexReadNames.html" title="BamIndexReadNames">bamindexreadnames</a></th><td>Build a dictionary of read names to be searched with BamQueryReadNames</td><td/><td/><td/></tr>
<tr id="bamtreepack"><th><a href="BamTreePack.html" title="BamTreePack">bamtreepack</a></th><td>Create a TreeMap from one or more SAM/BAM file. Ouput is a SVG file.</td><td>bam treepack</td><td/><td/></tr>
<tr id="fastqrecordtreepack"><th><a href="FastqRecordTreePack.html" title="FastqRecordTreePack">fastqrecordtreepack</a></th><td>Create a TreeMap from one or more Fastq file. Ouput is a SVG file</td><td/><td/><td/></tr>
<tr id="samfindclippedregions"><th><a href="SamFindClippedRegions.html" title="SamFindClippedRegions">samfindclippedregions</a></th><td>Fins clipped position in one or more bam. </td><td>sam bam clip vcf</td><td/><td/></tr>
<tr id="vcftreepack"><th><a href="VcfTreePack.html" title="VcfTreePack">vcftreepack</a></th><td>Create a TreeMap from one or more VCF. Ouput is a SVG file.</td><td/><td/><td/></tr>
<tr id="vcfburdensplitter"><th><a href="VcfBurdenSplitter.html" title="VcfBurdenSplitter">vcfburdensplitter</a></th><td>Split VCF Using a Burden Splitter (by gene, transcript, etc..)</td><td/><td/><td/></tr>
<tr id="vcfburdenfisherv"><th><a href="VcfBurdenFisherV.html" title="VcfBurdenFisherV">vcfburdenfisherv</a></th><td>Fisher Case / Controls per Variant (Vertical)</td><td>vcf burden fisher</td><td/><td/></tr>
<tr id="vcfburdenrscriptv"><th><a href="VcfBurdenRscriptV.html" title="VcfBurdenRscriptV">vcfburdenrscriptv</a></th><td>Fisher Case / Controls per Variant (Vertical)</td><td>vcf burden fisher</td><td/><td/></tr>
<tr id="vcfderby01"><th><a href="VcfDerby01.html" title="VcfDerby01">vcfderby01</a></th><td>Insert similar VCFs into an Apache Derby Database</td><td>vcf sql derby burden</td><td/><td/></tr>
<tr id="vcfdoest"><th><a href="VcfDoest.html" title="VcfDoest">vcfdoest</a></th><td>generate Transcript information for DOEST test</td><td>vcf burden doest</td><td/><td/></tr>
<tr id="bioalcidae"><th><a href="BioAlcidae.html" title="BioAlcidae">bioalcidae</a></th><td>javascript version of awk for bioinformatics</td><td>sam bam vcf javascript js nashorn</td><td/><td/></tr>
<tr id="picardmetrics2xml"><th><a href="PicardMetricsToXML.html" title="PicardMetricsToXML">picardmetrics2xml</a></th><td>transforms a picard metrics file to XML. See http://plindenbaum.blogspot.fr/2013/02/making-use-of-picard-metrics-files.html</td><td>picard xml metrics</td><td/><td/></tr>
<tr id="casectrlcanvas"><th><a href="CaseControlCanvas.html" title="CaseControlCanvas">casectrlcanvas</a></th><td>draw a chart of case/control maf from a stream of X/Y values</td><td>vcf case control visualization jfx chart maf</td><td/><td/></tr>
<tr id="lowresbam2raster"><th><a href="LowResBam2Raster.html" title="LowResBam2Raster">lowresbam2raster</a></th><td>Low Resolution BAM to raster graphics</td><td>bam alignment graphics visualization png gtf</td><td/><td/></tr>
<tr id=""><th><a href="BamQueryReadNames.html" title="BamQueryReadNames"/></th><td>Query a Bam file indexed with BamIndexReadNames</td><td/><td/><td/></tr>
<tr id="knime2txt"><th><a href="KnimeToText.html" title="KnimeToText">knime2txt</a></th><td>converts a Knime Workflow to a html representation.</td><td>knime workflow convert</td><td/><td/></tr>
<tr id="lumpyvcf2circos"><th><a href="LumpyVcfToCircos.html" title="LumpyVcfToCircos">lumpyvcf2circos</a></th><td>Lumpy to Circos</td><td>lumpy circos sv vcf</td><td/><td/></tr>
<tr id="genscan"><th><a href="GenScan.html" title="GenScan">genscan</a></th><td>Paint a Genome Scan picture from a Tab delimited file (CHROM/POS/VALUE1/VALUE2/....).</td><td>chromosome reference chart visualization</td><td/><td/></tr>
<tr id="vcfucsc"><th><a href="VcfUcsc.html" title="VcfUcsc">vcfucsc</a></th><td>annotate an VCF with mysql UCSC data</td><td>ucsc mysql vcf</td><td/><td/></tr>
<tr id="xsltstream"><th><a href="XsltStream.html" title="XsltStream">xsltstream</a></th><td>XSLT transformation for large XML files. xslt is only applied on a given subset of nodes.</td><td>xml xslt xsl stylesheet</td><td/><td/></tr>
<tr id="vcfloopovergenes"><th><a href="VcfLoopOverGenes.html" title="VcfLoopOverGenes">vcfloopovergenes</a></th><td>Generates a BED file of the Genes in an annotated VCF, loop over those genes and generate a VCF for each gene, then execute an optional command.</td><td>vcf gene burden</td><td/><td/></tr>
<tr id="vcffilterjdk"><th><a href="VcfFilterJdk.html" title="VcfFilterJdk">vcffilterjdk</a></th><td>Filtering VCF with dynamically-compiled java expressions</td><td>vcf filter java jdk</td><td/><td/></tr>
<tr id="optimizer"><th><a href="Optimizer.html" title="Optimizer">optimizer</a></th><td>Genetic-Programming-like parameters optimizer</td><td>genetic-programming</td><td/><td/></tr>
<tr id="bioalcidaejdk"><th><a href="BioAlcidaeJdk.html" title="BioAlcidaeJdk">bioalcidaejdk</a></th><td>java-based version of awk for bioinformatics</td><td>sam bam vcf java jdk gtf</td><td/><td/></tr>
<tr id="copynumber01"><th><a href="CopyNumber01.html" title="CopyNumber01">copynumber01</a></th><td>experimental CNV detection.</td><td>cnv bam sam</td><td/><td/></tr>
<tr id="samjdk"><th><a href="SamJdk.html" title="SamJdk">samjdk</a></th><td>Filters a BAM using a java expression compiled in memory.</td><td>sam bam java jdk filter</td><td/><td/></tr>
<tr id="vcfmakedict"><th><a href="VcfCreateDictionary.html" title="VcfCreateDictionary">vcfmakedict</a></th><td>Create a SAM Sequence Dictionary from a set of VCF files.</td><td>vcf dict fai</td><td/><td/></tr>
<tr id="vcfbigwig"><th><a href="VCFBigWig.html" title="VCFBigWig">vcfbigwig</a></th><td>Annotate a VCF with values from a bigwig file</td><td>vcf wig wiggle bigwig</td><td/><td/></tr>
<tr id="vcfnocall2homref"><th><a href="VcfNoCallToHomRef.html" title="VcfNoCallToHomRef">vcfnocall2homref</a></th><td>Convert the UNCALLED gentoypes in a VCF to HOM_REF. This tool can be used after using GATK CombineVariants.</td><td>vcf</td><td/><td><span style="color:orange;" title="deprecated">use bcftools plugin: +setGT</span>. </td></tr>
<tr id="gff2kg"><th><a href="Gff2KnownGene.html" title="Gff2KnownGene">gff2kg</a></th><td>Convert GFF3/GTF format to UCSC knownGene format.</td><td>gff ,gtf knownGene ucsc convert</td><td/><td/></tr>
<tr id="minicaller"><th><a href="MiniCaller.html" title="MiniCaller">minicaller</a></th><td>Simple and Stupid Variant Caller designed for @AdrienLeger2</td><td>bam sam calling vcf</td><td/><td/></tr>
<tr id="vcfoptimizeped4skat"><th><a href="VcfOptimizePedForSkat.html" title="VcfOptimizePedForSkat">vcfoptimizeped4skat</a></th><td>Optimize ped file for SKAT</td><td>vcf pedigree skat burden</td><td/><td/></tr>
<tr id="vcfskatslidingwindow"><th><a href="VcfSkatSlidingWindow.html" title="VcfSkatSlidingWindow">vcfskatslidingwindow</a></th><td>SkatFactory Over genome using a sliding window.</td><td>vcf pedigree skat burden</td><td/><td/></tr>
<tr id="vcfskat"><th><a href="VcfSkat.html" title="VcfSkat">vcfskat</a></th><td>Calculate SKAT score for a VCF.</td><td>vcf pedigree skat burden</td><td/><td/></tr>
<tr id="vcfserver"><th><a href="VcfServer.html" title="VcfServer">vcfserver</a></th><td>Web Server displaying VCF file. A web interface for vcf2table</td><td>vcf table visualization server web</td><td/><td/></tr>
<tr id="tviewserver"><th><a href="TViewServer.html" title="TViewServer">tviewserver</a></th><td>Web Server displaying SAM/BAM file. A web interface for jvarkit:tview</td><td>sam bam table visualization server web</td><td/><td/></tr>
<tr id="pubmedgraph"><th><a href="PubmedGraph.html" title="PubmedGraph">pubmedgraph</a></th><td>Creates a Gephi-gexf graph of references-cites for a given PMID</td><td>pubmed xml graph</td><td/><td/></tr>
<tr id="vcftrap"><th><a href="VcfTrap.html" title="VcfTrap">vcftrap</a></th><td>annotate vcf with trap database http://trap-score.org/</td><td>vcf trap annotation</td><td/><td/></tr>
<tr id="trapindexer"><th><a href="TrapIndexer.html" title="TrapIndexer">trapindexer</a></th><td>Convert text data to binary format for the trap DATABASE database http://trap-score.org/. Those data can be used by the tool `vcftrap`.</td><td>trap</td><td/><td/></tr>
<tr id="prettysam"><th><a href="PrettySam.html" title="PrettySam">prettysam</a></th><td>Pretty SAM alignments</td><td>sam bam</td><td/><td/></tr>
<tr id="vcfremoveunusedalt"><th><a href="VcfRemoveUnusedAlt.html" title="VcfRemoveUnusedAlt">vcfremoveunusedalt</a></th><td>Remove unused ALT allele if there is no genotype with this alt, or there is no sample but AC=0</td><td>vcf genotype</td><td/><td/></tr>
<tr id="variantsinwindow"><th><a href="VariantsInWindow.html" title="VariantsInWindow">variantsinwindow</a></th><td>Annotate Number of Variants overlaping a sliding window.</td><td>vcf annotation</td><td/><td/></tr>
<tr id="samaddpi"><th><a href="SamAddPI.html" title="SamAddPI">samaddpi</a></th><td>Add predicted median insert size 'PI' to SAM Read groups (RG).</td><td>sam bam</td><td/><td/></tr>
<tr id="goutils"><th><a href="GoUtils.html" title="GoUtils">goutils</a></th><td>Gene Ontology Utils. Retrieves terms from Gene Ontology</td><td>geneontology go gexf</td><td/><td/></tr>
<tr id="indexcovjfx"><th><a href="IndexCovJfx.html" title="IndexCovJfx">indexcovjfx</a></th><td>display indexcov data in a jfx client</td><td>cnv jfx duplication deletion sv</td><td/><td/></tr>
<tr id="indexcov2vcf"><th><a href="IndexCovToVcf.html" title="IndexCovToVcf">indexcov2vcf</a></th><td>convert indexcov data to vcf</td><td>cnv duplication deletion sv indexcov</td><td/><td/></tr>
<tr id="tview"><th><a href="TViewCmd.html" title="TViewCmd">tview</a></th><td>equivalent of samtools tview</td><td>sam bam visualization terminal</td><td/><td/></tr>
<tr id="samcustomsortjdk"><th><a href="SamCustomSortJdk.html" title="SamCustomSortJdk">samcustomsortjdk</a></th><td>Sort a BAM file using a java expression compiled at runtime.</td><td>sam bam java jdk sort</td><td/><td/></tr>
<tr id="simpleplot"><th><a href="SimplePlot.html" title="SimplePlot">simpleplot</a></th><td>simple figure plotter output is a R script</td><td>char figure</td><td/><td/></tr>
<tr id="cytoband2svg"><th><a href="CytobandToSvg.html" title="CytobandToSvg">cytoband2svg</a></th><td>Creates a svg karyotype .</td><td>karyotype svg ideogram</td><td/><td/></tr>
<tr id="vcfstatsjfx"><th><a href="VcfStatsJfx.html" title="VcfStatsJfx">vcfstatsjfx</a></th><td>VCF statistics</td><td>vcf stats</td><td/><td/></tr>
<tr id="vcfancestralalleles"><th><a href="VcfAncestralAllele.html" title="VcfAncestralAllele">vcfancestralalleles</a></th><td>Annotate a VCF with it's ancestral allele. Data from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.README</td><td>vcf ancestral 1000k allele</td><td/><td/></tr>
<tr id="vcfgo"><th><a href="VcfGeneOntology.html" title="VcfGeneOntology">vcfgo</a></th><td>Find the GO terms for VCF annotated with SNPEFF or VEP</td><td>vcf go</td><td/><td><span style="color:orange;" title="deprecated">do not use this</span>. </td></tr>
<tr id="vcfcomparecallersonesample"><th><a href="VcfCompareCallersOneSample.html" title="VcfCompareCallersOneSample">vcfcomparecallersonesample</a></th><td>For my colleague Julien: VCF with one sample called using different callers. Only keep variant if it was found in min&lt;x=other-files&lt;=max</td><td>vcf compare</td><td/><td/></tr>
<tr id="bednonoverlappingset"><th><a href="BedNonOverlappingSet.html" title="BedNonOverlappingSet">bednonoverlappingset</a></th><td>Split a Bed file into non-overlapping data set.</td><td>bed</td><td/><td/></tr>
<tr id="vcfafinfofilter"><th><a href="VcfAfInfoFilter.html" title="VcfAfInfoFilter">vcfafinfofilter</a></th><td>Filter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomad</td><td>vcf annotation af</td><td/><td/></tr>
<tr id="biostar322664"><th><a href="Biostar322664.html" title="Biostar322664">biostar322664</a></th><td>Extract PE Reads (with their mates) supporting variants in vcf file</td><td>sam bam vcf</td><td/><td/></tr>
<tr id="vcfcomposite"><th><a href="VCFComposite.html" title="VCFComposite">vcfcomposite</a></th><td>(in developpement) Finds Variants involved in a Het Compound Disease</td><td>vcf disease annotation pedigree haplotype</td><td/><td/></tr>
<tr id="biostar92368"><th><a href="Biostar92368.html" title="Biostar92368">biostar92368</a></th><td>Binary interactions depth.</td><td>protein interaction interactome</td><td/><td/></tr>
<tr id="wescnvsvg"><th><a href="WesCnvSvg.html" title="WesCnvSvg">wescnvsvg</a></th><td>SVG visualization of bam DEPTH for multiple regions</td><td>bam alignment graphics visualization svg wes bed capture exome</td><td/><td/></tr>
<tr id="naivecnvdetector"><th><a href="NaiveCnvDetector.html" title="NaiveCnvDetector">naivecnvdetector</a></th><td>experimental CNV detection for multiple samples.</td><td>cnv bam sam wig bigwig bigbed</td><td/><td/></tr>
<tr id="vcfclusteredreadedge"><th><a href="VcfClusteredReadEdge.html" title="VcfClusteredReadEdge">vcfclusteredreadedge</a></th><td>Variant annotation :   variants clustered near the ends of reads</td><td>sam bam vcf</td><td/><td/></tr>
<tr id="biostar332826"><th><a href="Biostar332826.html" title="Biostar332826">biostar332826</a></th><td>Fast Extraction of Variants from a list of IDs</td><td>vcf rs id</td><td/><td/></tr>
<tr id="pubmedauthorgraph"><th><a href="PubmedAuthorGraph.html" title="PubmedAuthorGraph">pubmedauthorgraph</a></th><td>Creates a graph from Pubmed and Authors</td><td>pubmed ncbi graph</td><td/><td/></tr>
<tr id="gephicmd"><th><a href="GephiCmd.html" title="GephiCmd">gephicmd</a></th><td>Cmd-line oriented for gephi.</td><td>graph gexf gephi visualization</td><td/><td/></tr>
<tr id="gexftr"><th><a href="GexfTransformer.html" title="GexfTransformer">gexftr</a></th><td>Gexf file manipulation</td><td>gexf graph network</td><td/><td/></tr>
<tr id="ncbigenedump"><th><a href="NcbiGeneDump.html" title="NcbiGeneDump">ncbigenedump</a></th><td>Dump XML results from a list of gene using NCBI/Eutils</td><td>ncbi gene xml</td><td/><td/></tr>
<tr id="vcfallelebalance"><th><a href="VcfAlleleBalance.html" title="VcfAlleleBalance">vcfallelebalance</a></th><td>Insert missing allele balance annotation using FORMAT:AD</td><td>vcf allele-balance depth</td><td/><td/></tr>
<tr id="vcfgapfrequent"><th><a href="VcfGapFrequent.html" title="VcfGapFrequent">vcfgapfrequent</a></th><td>Filter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomad</td><td>vcf</td><td/><td/></tr>
<tr id="biostar336589"><th><a href="Biostar336589.html" title="Biostar336589">biostar336589</a></th><td>displays circular map as SVG from BED and REF file</td><td>genome browser circular bed svg</td><td/><td/></tr>
<tr id="bamslicebed"><th><a href="BamSliceBed.html" title="BamSliceBed">bamslicebed</a></th><td>For @wouter_decoster : slice (long reads) overlapping the records of a BED file</td><td>sam bam bed</td><td/><td/></tr>
<tr id="mergecnvnator"><th><a href="MergeCnvNator.html" title="MergeCnvNator">mergecnvnator</a></th><td>Merge CNVNator results</td><td>cnv indel cnvnator</td><td/><td/></tr>
<tr id="faidxsplitter"><th><a href="FaidxSplitter.html" title="FaidxSplitter">faidxsplitter</a></th><td>Split bed of reference genome into overlapping parts</td><td>vcf reference bed</td><td/><td/></tr>
<tr id="cnvtview"><th><a href="CnvTView.html" title="CnvTView">cnvtview</a></th><td>Text visualization of bam DEPTH for multiple regions in a terminal</td><td>bam alignment graphics visualization cnv ascii text</td><td/><td/></tr>
<tr id="sv2svg"><th><a href="SvToSVG.html" title="SvToSVG">sv2svg</a></th><td>BAM to SVG. Used to display structural variations.</td><td>bam alignment graphics visualization svg structural variant</td><td/><td/></tr>
<tr id="vcf2bed"><th><a href="VcfToBed.html" title="VcfToBed">vcf2bed</a></th><td>vcf to bed</td><td>bed vcf</td><td/><td/></tr>
<tr id="biostar352930"><th><a href="Biostar352930.html" title="Biostar352930">biostar352930</a></th><td>Fills the empty SEQ(*) and QUAL(*) in a bam file using the the reads with the same name carrying this information.</td><td>sam bam</td><td/><td/></tr>
<tr id="pubmed404"><th><a href="Pubmed404.html" title="Pubmed404">pubmed404</a></th><td>Test if URL in the pubmed abstracts are reacheable.</td><td>pubmed url</td><td/><td/></tr>
<tr id="vcfstrechofgt"><th><a href="VcfStretchOfGt.html" title="VcfStretchOfGt">vcfstrechofgt</a></th><td>Try to finds deletion by searching strech of HOM_REF/HOM_VAR/NO_CALL Genotypes.</td><td>vcf deletion cnv</td><td/><td/></tr>
<tr id="haloplexparasite"><th><a href="HaloplexParasite.html" title="HaloplexParasite">haloplexparasite</a></th><td>for @SolenaLS : remove artctifacts from haloplex that gives indels in GATK hapcaller </td><td>vcf haloplex</td><td/><td/></tr>
<tr id="ngsfilesscanner"><th><a href="NgsFilesScanner.html" title="NgsFilesScanner">ngsfilesscanner</a></th><td>Build a persistent database of NGS file. Dump as XML.</td><td>ngs bam sam vcf xml</td><td/><td/></tr>
<tr id="vcfburdensplitter2"><th><a href="VcfBurdenSplitter2.html" title="VcfBurdenSplitter2">vcfburdensplitter2</a></th><td>new version</td><td>vcf burden gene vep snpeff prediction</td><td/><td/></tr>
<tr id="vcfensemblreg"><th><a href="VcfEnsemblReg.html" title="VcfEnsemblReg">vcfensemblreg</a></th><td>Annotate a VCF with the UCSC genome hub tracks for Ensembl Regulation.</td><td>vcf ensembl regulation</td><td/><td/></tr>
<tr id="scanretrocopy"><th><a href="ScanRetroCopy.html" title="ScanRetroCopy">scanretrocopy</a></th><td>Scan BAM for retrocopies</td><td>sam bam cigar clip sv retrocopy</td><td/><td/></tr>
<tr id="sigframe"><th><a href="Main.html" title="Main">sigframe</a></th><td>SigFrame displays CGH/ position+values in a GUI</td><td>cgh gui visualization</td><td/><td/></tr>
<tr id="samviewwithmate"><th><a href="SamViewWithMate.html" title="SamViewWithMate">samviewwithmate</a></th><td>Extract reads within given region(s), and their mates</td><td>sam bam</td><td/><td/></tr>
<tr id="kg2fa"><th><a href="KnownGeneToFasta.html" title="KnownGeneToFasta">kg2fa</a></th><td>convert knownGenes to fasta</td><td>kg knownGene fasta</td><td/><td/></tr>
<tr id="vcfscanupstreamorf"><th><a href="VcfScanUpstreamOrf.html" title="VcfScanUpstreamOrf">vcfscanupstreamorf</a></th><td>Scan BAM for upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs </td><td>vcf uorf</td><td/><td/></tr>
<tr id="vcfgnomadpext"><th><a href="VcfGnomadPext.html" title="VcfGnomadPext">vcfgnomadpext</a></th><td>Peek annotations from gnomadpext</td><td>vcf annotation gnomad</td><td/><td/></tr>
<tr id="vcfsparql"><th><a href="VcfSparql.html" title="VcfSparql">vcfsparql</a></th><td>Query RDF with Sparql. Very slow. Just a proof of concept</td><td>vcf sparql rdf arq semanticweb</td><td/><td/></tr>
<tr id="samtranslocations"><th><a href="SamTranslocations.html" title="SamTranslocations">samtranslocations</a></th><td>Explore balanced translocations between two chromosomes using discordant paired-end reads.</td><td>sam bam sv translocation</td><td/><td/></tr>
<tr id="convertliftoverchain"><th><a href="ConvertLiftOverChain.html" title="ConvertLiftOverChain">convertliftoverchain</a></th><td>Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...)</td><td>chain liftover</td><td/><td/></tr>
<tr id="mkminibam"><th><a href="MakeMiniBam.html" title="MakeMiniBam">mkminibam</a></th><td>Creates an archive of small bams with only a few regions.</td><td>bam sam</td><td/><td/></tr>
<tr id="vcfdistancevariants"><th><a href="VcfDistanceBetweenVariants.html" title="VcfDistanceBetweenVariants">vcfdistancevariants</a></th><td>Annotate variants with the distance between previous and next variant.</td><td>vcf annotation distance</td><td/><td/></tr>
<tr id="hicfileinfo"><th><a href="HicFileInfo.html" title="HicFileInfo">hicfileinfo</a></th><td>Prints information about a HI-C File/URL</td><td>hic</td><td/><td/></tr>
<tr id="vcfwindowsplitter"><th><a href="VcfSlidingWindowSplitter.html" title="VcfSlidingWindowSplitter">vcfwindowsplitter</a></th><td>Split VCF by sliding window</td><td>vcf sliding window</td><td/><td/></tr>
<tr id="bammatrix"><th><a href="BamMatrix.html" title="BamMatrix">bammatrix</a></th><td>Bam matrix, inspired from 10x/loupe </td><td>sam bam compare matrix</td><td/><td/></tr>
<tr id="vcfphased01"><th><a href="VcfPhased01.html" title="VcfPhased01">vcfphased01</a></th><td>X10 Phased SVG to Scalar Vector Graphics (SVG)</td><td>x10 phased genotypes svg</td><td/><td/></tr>
<tr id="starretrocopy"><th><a href="StarRetroCopy.html" title="StarRetroCopy">starretrocopy</a></th><td>Scan retrocopies from the star-aligner/bwa output</td><td>sam bam cigar clip sv retrocopy star</td><td/><td/></tr>
<tr id="ijgv2vcf"><th><a href="IjgvdToVcf.html" title="IjgvdToVcf">ijgv2vcf</a></th><td>Convert zips of Integrative Japanese Genome Variation to VCF file.</td><td>vcf jgvd japan tommo</td><td/><td><span style="color:orange;" title="deprecated">Deprecated since data are now available as VCF</span>. </td></tr>
<tr id="vcfadfraction"><th><a href="VcfAlleleDepthFraction.html" title="VcfAlleleDepthFraction">vcfadfraction</a></th><td>filter VCF for strange FORMAT:AD fraction</td><td>vcf allele-balance depth</td><td/><td/></tr>
<tr id="gtfsplitter"><th><a href="GtfFileSplitter.html" title="GtfFileSplitter">gtfsplitter</a></th><td>Split GTF file per gene, transcript, chromosome...</td><td>gtf</td><td/><td/></tr>
<tr id="gtfretrocopy"><th><a href="GtfRetroCopy.html" title="GtfRetroCopy">gtfretrocopy</a></th><td>Scan retrocopies by comparing the gtf/intron and the deletions in a VCF</td><td>gtf retrocopy deletion</td><td/><td/></tr>
<tr id="vcfgnomadsv"><th><a href="VcfGnomadSV.html" title="VcfGnomadSV">vcfgnomadsv</a></th><td>Peek annotations from gnomad structural variants</td><td>vcf annotation gnomad sv</td><td/><td/></tr>
<tr id="knownretrocopy"><th><a href="KnownRetroCopy.html" title="KnownRetroCopy">knownretrocopy</a></th><td>Annotate VCF structural variants that could be intron from retrocopies.</td><td>gtf retrocopy deletion</td><td/><td/></tr>
<tr id="svpredictions"><th><a href="SVPredictions.html" title="SVPredictions">svpredictions</a></th><td>Basic Variant Effect prediction using gtf</td><td>vcf annotation prediction sv</td><td/><td/></tr>
<tr id="gtfliftover"><th><a href="GtfLiftOver.html" title="GtfLiftOver">gtfliftover</a></th><td>LiftOver GTF file.</td><td>gtf liftover</td><td/><td/></tr>
<tr id="scansv"><th><a href="ScanStructuralVariants.html" title="ScanStructuralVariants">scansv</a></th><td>Scan structural variants for case/controls data</td><td>cnv indel sv pedigree</td><td/><td/></tr>
<tr id="bamheteroplasmy"><th><a href="BamHeteroplasmy.html" title="BamHeteroplasmy">bamheteroplasmy</a></th><td>Call a VCF for the Mitochondria (Experimental)</td><td>vcf sam bam mitochondria</td><td/><td/></tr>
<tr id="findhtsfiledict"><th><a href="FindHtsFileDictionary.html" title="FindHtsFileDictionary">findhtsfiledict</a></th><td>Scan a set of HTS files (VCF, BAM, CRAM), return a tab delimited file (path-of-file,path-to-fasta)</td><td>sam bam cram vcf dict</td><td/><td/></tr>
<tr id="biostar398854"><th><a href="Biostar398854.html" title="Biostar398854">biostar398854</a></th><td>Extract every CDS sequences from a VCF file</td><td>vcf gtf</td><td/><td/></tr>
<tr id="psl2bam"><th><a href="PslxToBam.html" title="PslxToBam">psl2bam</a></th><td>Convert PSL to SAM/BAM</td><td>blat sam bam psl pslx</td><td/><td/></tr>
<tr id="mantamerger"><th><a href="MantaMerger.html" title="MantaMerger">mantamerger</a></th><td>Merge Vcf from Manta VCF.</td><td>sv burden manta vcf</td><td/><td/></tr>
<tr id="vcfburdenslidingwindow"><th><a href="VcfBurdenSlidingWindow.html" title="VcfBurdenSlidingWindow">vcfburdenslidingwindow</a></th><td>Run Burden Sliding window</td><td>vcf burden case control</td><td/><td/></tr>
<tr id="depthofcoverage"><th><a href="DepthOfCoverage.html" title="DepthOfCoverage">depthofcoverage</a></th><td>A custom 'Depth of Coverage'.</td><td>depth bam sam coverage</td><td/><td/></tr>
<tr id="biostar404363"><th><a href="Biostar404363.html" title="Biostar404363">biostar404363</a></th><td>introduce artificial mutation SNV in bam</td><td>sam bam variant</td><td/><td/></tr>
<tr id="hmmmergebed"><th><a href="HmmMergeBed.html" title="HmmMergeBed">hmmmergebed</a></th><td>For @154sns. Merge hmm bed</td><td>bed merge</td><td/><td/></tr>
<tr id="vcfrebase"><th><a href="VcfRebase.html" title="VcfRebase">vcfrebase</a></th><td>Restriction sites overlaping variations in a vcf</td><td>vcf rebase restriction enzyme</td><td/><td/></tr>
<tr id="vcfgtfsplitter"><th><a href="VcfGtfSplitter.html" title="VcfGtfSplitter">vcfgtfsplitter</a></th><td>Split VCF+VEP by gene/transcript using a GTF file.</td><td>genes vcf split gtf</td><td/><td/></tr>
<tr id="vcfpeekaf"><th><a href="VcfPeekAf.html" title="VcfPeekAf">vcfpeekaf</a></th><td>Peek the AF from another VCF</td><td>vcf annotation af</td><td/><td/></tr>
<tr id="plotsashimi"><th><a href="PlotSashimi.html" title="PlotSashimi">plotsashimi</a></th><td>Print Sashimi plots from Bam</td><td>bam visualization svg rna exon rnaseq</td><td/><td/></tr>
<tr id="bamwithoutbai"><th><a href="BamWithoutBai.html" title="BamWithoutBai">bamwithoutbai</a></th><td>Query a Remote BAM without bai</td><td>bam sam bai remote</td><td/><td/></tr>
<tr id="bedcluster"><th><a href="BedCluster.html" title="BedCluster">bedcluster</a></th><td>Clusters a BED file into a set of BED files.</td><td>bed chromosome contig</td><td/><td/></tr>
<tr id="coverageserver"><th><a href="CoverageServer.html" title="CoverageServer">coverageserver</a></th><td>Jetty Based http server serving Bam coverage.</td><td>cnv bam coverage server</td><td/><td/></tr>
<tr id="fastqsplit"><th><a href="FastqSplit.html" title="FastqSplit">fastqsplit</a></th><td>Split Fastq files into multiple files.</td><td>fastq</td><td/><td/></tr>
<tr id="bedmergecnv"><th><a href="BedMergeCnv.html" title="BedMergeCnv">bedmergecnv</a></th><td>Merge Bed records if they overlap a fraction of their lengths.</td><td>bed chromosome contig</td><td/><td/></tr>
<tr id="validatecnv"><th><a href="ValidateCnv.html" title="ValidateCnv">validatecnv</a></th><td>Experimental CNV Genotyping. Look variance of depths before/after putative known CNV.</td><td>cnv bam sam vcf depth</td><td/><td/></tr>
<tr id="htsfileserver"><th><a href="HtsFileServer.html" title="HtsFileServer">htsfileserver</a></th><td>Jetty Based http server serving Vcf and Bam files.</td><td>vcf bam server</td><td/><td/></tr>
<tr id="breakdancer2vcf"><th><a href="BreakdancerToVcf.html" title="BreakdancerToVcf">breakdancer2vcf</a></th><td>Convert output of breakdancer to VCF</td><td>cnv sv breakdancer vcf</td><td/><td/></tr>
<tr id="indexcov2sv"><th><a href="IndexCovToSV.html" title="IndexCovToSV">indexcov2sv</a></th><td>same as indexcov2vcf but merge segments</td><td>cnv duplication deletion sv indexcov</td><td/><td/></tr>
<tr id="vcfpostprocesssv"><th><a href="VcfPostProcessSV.html" title="VcfPostProcessSV">vcfpostprocesssv</a></th><td>Postprocess BND pairs in a MANTA/LUMPY-SV.</td><td>cnv sv gidss vcf</td><td/><td/></tr>
<tr id="coverageplotter"><th><a href="CoveragePlotter.html" title="CoveragePlotter">coverageplotter</a></th><td>Find anomaly of depth in intervals+bams</td><td>cnv bam depth coverage</td><td/><td/></tr>
<tr id="bamallelebalance"><th><a href="BamAlleleBalance.html" title="BamAlleleBalance">bamallelebalance</a></th><td>Compute statistics about allele balance from a set of Bams</td><td>vcf allele-balance depth bam</td><td/><td/></tr>
<tr id="vcfpar"><th><a href="VcfPseudoAutosomalRegion.html" title="VcfPseudoAutosomalRegion">vcfpar</a></th><td>Flag human sexual regions excluding PAR.</td><td>vcf sex par</td><td/><td/></tr>
<tr id="combinevcffisher"><th><a href="CombineVcfFisher.html" title="CombineVcfFisher">combinevcffisher</a></th><td>Combine multiple VCF to perform a 'vertical' fisher test.</td><td>vcf burden fisher</td><td/><td/></tr>
<tr id="vcfbraiding"><th><a href="VcfBraiding.html" title="VcfBraiding">vcfbraiding</a></th><td>visualization for variants and attributes using https://visdunneright.github.io/sequence_braiding/docs/ .</td><td>vcf visualization</td><td/><td/></tr>
<tr id="vcfspliceai"><th><a href="VcfSpliceAI.html" title="VcfSpliceAI">vcfspliceai</a></th><td>Annotate VCF with spiceai web service</td><td>vcf splice splicing spliceai</td><td/><td/></tr>
<tr id="wgscoverageplotter"><th><a href="WGSCoveragePlotter.html" title="WGSCoveragePlotter">wgscoverageplotter</a></th><td>Whole genome coverage plotter</td><td>svg bam depth coverage</td><td/><td/></tr>
<tr id="biostar480685"><th><a href="Biostar480685.html" title="Biostar480685">biostar480685</a></th><td>paired-end bam clip bases outside insert range</td><td>sam bam clip</td><td/><td/></tr>
<tr id="kg2gff"><th><a href="KgToGff.html" title="KgToGff">kg2gff</a></th><td>Convert UCSC knowGene file to gff3</td><td>gff gff3 ucsc</td><td/><td/></tr>
<tr id="biostar489074"><th><a href="Biostar489074.html" title="Biostar489074">biostar489074</a></th><td>call variants for every paired overlaping read</td><td>sam bam vcf call</td><td/><td/></tr>
<tr id="expansionhuntermerge"><th><a href="ExpansionHunterMerge.html" title="ExpansionHunterMerge">expansionhuntermerge</a></th><td>Merge Vcf from ExpansionHunter.</td><td>vcf merge ExpansionHunter</td><td/><td/></tr>
<tr id="bamphased01"><th><a href="BamPhased01.html" title="BamPhased01">bamphased01</a></th><td>Extract Reads from a SAM/BAM file supporting at least two variants in a VCF file.</td><td>vcf phased genotypes bam</td><td/><td/></tr>
<tr id="vcfstrech2svg"><th><a href="VcfStrechToSvg.html" title="VcfStrechToSvg">vcfstrech2svg</a></th><td>another VCF to SVG</td><td>vcf deletion cnv svg</td><td/><td/></tr>
<tr id="biostar497922"><th><a href="Biostar497922.html" title="Biostar497922">biostar497922</a></th><td>Split VCF into separate VCFs by SNP count</td><td>vcf</td><td/><td/></tr>
<tr id="biostar9462889"><th><a href="Biostar9462889.html" title="Biostar9462889">biostar9462889</a></th><td>Extracting reads from a regular expression in a bam file</td><td>sam bam split util</td><td/><td/></tr>
<tr id="swingbamcov"><th><a href="SwingBamCov.html" title="SwingBamCov">swingbamcov</a></th><td>Bam coverage viewer using Java Swing UI</td><td>bam alignment graphics visualization swing</td><td/><td/></tr>
<tr id="swingvcfview"><th><a href="SwingVcfView.html" title="SwingVcfView">swingvcfview</a></th><td>VCFviewer using Java Swing UI</td><td>vcf visualization swing</td><td/><td/></tr>
<tr id="bamxtremdepth"><th><a href="BamXtremDepth.html" title="BamXtremDepth">bamxtremdepth</a></th><td>Compute low and high depth shared by a set of BAM files</td><td>bam depth coverage</td><td/><td/></tr>
<tr id="biostar9469733"><th><a href="Biostar9469733.html" title="Biostar9469733">biostar9469733</a></th><td>Extract reads mapped within chosen intronic region from BAM file</td><td>sam bam rnaseq bed</td><td/><td/></tr>
<tr id="vcffilterbyliftover"><th><a href="VcfFilterByLiftOver.html" title="VcfFilterByLiftOver">vcffilterbyliftover</a></th><td>Add FILTER(s) to a variant when it is known to map elsewhere after liftover.</td><td>vcf liftover</td><td/><td/></tr>
<tr id="builddbsnp"><th><a href="BuildDbsnp.html" title="BuildDbsnp">builddbsnp</a></th><td>Build a DBSNP file from different sources for GATK</td><td>vcf dbsnp</td><td/><td/></tr>
<tr id="iranomescrapper"><th><a href="IranomeScrapper.html" title="IranomeScrapper">iranomescrapper</a></th><td>Iranome scrapper</td><td>iranome vcf</td><td/><td/></tr>
<tr id="ukbiobanksamples"><th><a href="UKBiobankSelectSamples.html" title="UKBiobankSelectSamples">ukbiobanksamples</a></th><td>Select samples from ukbiobank</td><td>ukbiobank</td><td/><td/></tr>
<tr id="findgvcfsblocks"><th><a href="FindGVCFsBlocks.html" title="FindGVCFsBlocks">findgvcfsblocks</a></th><td>Find common blocks of calleable regions from a set of gvcfs</td><td>gvcf gatk vcf</td><td/><td/></tr>
<tr id="rnaseqpolya"><th><a href="RNASeqPolyA.html" title="RNASeqPolyA">rnaseqpolya</a></th><td>find poly-A tail in RNASeq data</td><td>bam sam rnaseq polya</td><td/><td/></tr>
<tr id="bam2haplotypes"><th><a href="BamToHaplotypes.html" title="BamToHaplotypes">bam2haplotypes</a></th><td>Reconstruct SNP haplotypes from reads</td><td>vcf phased genotypes bam</td><td/><td/></tr>
<tr id="mergesv"><th><a href="MergeStructuralVariants.html" title="MergeStructuralVariants">mergesv</a></th><td>Experimental SV/CNV merger.</td><td>cnv indel sv</td><td/><td/></tr>
<tr id="vcf2intervals"><th><a href="VcfToIntervals.html" title="VcfToIntervals">vcf2intervals</a></th><td>split a vcf to interval or bed for parallelization</td><td>vcf bed interval</td><td/><td/></tr>
<tr id="vcfroh"><th><a href="VcfROH.html" title="VcfROH">vcfroh</a></th><td>VCF ROH</td><td>vcf roh</td><td/><td/></tr>
<tr id="biostar9501110"><th><a href="Biostar9501110.html" title="Biostar9501110">biostar9501110</a></th><td>Keep reads including/excluding variants from VCF</td><td>sam bam vcf</td><td/><td/></tr>
<tr id="vcfbigbed"><th><a href="VcfBigBed.html" title="VcfBigBed">vcfbigbed</a></th><td>Annotate a VCF with values from a bigbed file</td><td>vcf wig wiggle bigbed bed</td><td/><td/></tr>
</tbody>

</table>


<h2>Other Pages</h2>
<table>
<thead>
<tr>
		
		<th>Name</th>
		<th>Description</th>
		<th>Keywords</th>
		<th>Terms</th>
		<th>Misc</th>
</tr>
</thead>
<tbody>
	<tr><th><a href="KnimeIntegration.html" title="LowResBam2Raster">Knime Integration</a></th><td>How to use HTSJDK/Jvarkit in knime</td><td>bam sam knime vcf annotation</td><td/><td/></tr>
</tbody>
</table>
</div>

</body>

</html>